Abstract：
:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation. CpGenie produces allele-specific DNA methylation prediction with single-nucleotide sensitivity that enables accurate prediction of methylation quantitative trait loci (meQTL). We demonstrate that CpGenie prioritizes validated GWAS SNPs, and contributes to the prediction of functional non-coding variants, including expression quantitative trait loci (eQTL) and disease-associated mutations. CpGenie is publicly available to assist in identifying and interpreting regulatory non-coding variants.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zeng H,Gifford DKdoi
10.1093/nar/gkx177subject
Has Abstractpub_date
2017-06-20 00:00:00pages
e99issue
11eissn
0305-1048issn
1362-4962pii
3072752journal_volume
45pub_type
杂志文章abstract：:Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcript...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1071
更新日期：2011-01-01 00:00:00
abstract：:Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purifie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.4.787
更新日期：1997-02-15 00:00:00
abstract：:We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.19.7565
更新日期：1984-10-11 00:00:00
abstract：:We have constructed deletion mutants of simian virus 40 (SV40) lacking the two tandemly repeated copies or all three copies of the 21-bp repeated sequence located in the origin region. The mutants were viable, but had lower infectivities compared to the wild type. The mutant lacking two copies of the 21-bp repeat grew...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1601
更新日期：1983-03-11 00:00:00
abstract：:Cloned DNA from the EcoRI J fragment of EBV has been used as template for in vitro transcription experiments using cell-free extracts prepared from HeLa or KB cells. Two EBV specific RNAs each about 175 bases in length were synthesised and nuclease 51 mapping experiments determined that these in vitro products corresp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.11.3407
更新日期：1982-06-11 00:00:00
abstract：:Ethionamide is an antituberculous drug for the treatment of multidrug-resistant Mycobacterium tuberculosis. This antibiotic requires activation by the monooxygenase EthA to exert its activity. Production of EthA is controlled by the transcriptional repressor EthR, a member of the TetR family. The sensitivity of M. tub...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1113
更新日期：2012-04-01 00:00:00
abstract：:KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq943
更新日期：2011-01-01 00:00:00
abstract：:We have measured the amount of 5S-ribosomal DNA in the genomes of Xenopus laevis, Triturus cristatus carnifex and Ambystoma mexicanum, three species of Amphibians which have widely different C-values. Our best estimate is that these organisms have about 24,000, 32,000 and 61,000 5S-genes per haploid genome respectivel...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.8.2381
更新日期：1983-04-25 00:00:00
abstract：:Transfer RNAGlu4 was isolated from Drosophila melanogaster by affinity chromatography. The tRNA was iodinated "in vitro" with Na[25I] and hybridized "in situ" to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAGlu4 to the right arm of the second chro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.5.1465
更新日期：1978-05-01 00:00:00
abstract：:Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks906
更新日期：2012-12-01 00:00:00
abstract：:The transcription regulator, tvMyb1, is the first Myb family protein identified in Trichomonas vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence from Lys(35) to Ser(141) (tvMyb1(35-141)) as the minimal DNA-binding domain, encompassing two Myb-like DNA-binding motifs (designat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp097
更新日期：2009-04-01 00:00:00
abstract：:E2F transcription factors (E2F1-8) are known to coordinately regulate the expression of a plethora of target genes, including those coding for microRNAs (miRNAs), to control cell cycle progression. Recent work has described the atypical E2F factor E2F7 as a transcriptional repressor of cell cycle-related protein-codin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw146
更新日期：2016-07-08 00:00:00
abstract：:A method is described to simultaneously amplify and sequence DNA using a new class of nucleotides containing boron. During the polymerase chain reaction, boron-modified nucleotides, i.e. 2'-deoxynucleoside 5'-alpha-[P-borano]-triphosphates, are incorporated into the product DNA. The boranophosphate linkages are resist...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.8.1611
更新日期：1997-04-15 00:00:00
abstract：:In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.18.4344
更新日期：1993-09-11 00:00:00
abstract：:We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.13.2973
更新日期：1993-07-01 00:00:00
abstract：:Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structure...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.5.1297
更新日期：1979-11-10 00:00:00
abstract：:SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any tw...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl169
更新日期：2006-07-01 00:00:00
abstract：:A human term placental cDNA library was screened at low stringency with a human prolactin cDNA probe. One of the cDNAs isolated hybridizes to a 1.8 kb mRNA present in all four tissues of the placenta as well as to every nucleated tissue and cell line tested. The sequence of the full-length cDNA was determined. An exte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3871
更新日期：1990-07-11 00:00:00
abstract：:The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5469
更新日期：1981-10-24 00:00:00
abstract：:We report that greA expression is driven by two strong, overlapping P1 and P2 promoters. The P1 promoter is sigma(70)-dependent and P2 is sigma(E)-dependent. Two-thirds of transcripts terminate within the leader region and the remaining third comprises greA mRNA. Termination efficiency seems to be unaffected by growth...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1150
更新日期：2010-03-01 00:00:00
abstract：:Yeast tRNA Val 1 alkylation with 2', 3'-O-4-(N-2-chloroethyl-N-methylamino) benzylidene d(pC-G)-A proceeds at 20 degrees - 30 degrees C in the complementary complexes which are formed by d(pC-G)-A greater than RC1 binding to 3 sequences of tRNA Val 1 : psi-C-G58 in the T loop, C-G40 at the 3'-side of the anticodon loo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1609
更新日期：1977-01-01 00:00:00
abstract：:Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9631
更新日期：1988-10-25 00:00:00
abstract：:RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1045
更新日期：2013-01-01 00:00:00
abstract：:Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq030
更新日期：2010-06-01 00:00:00
abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf107
更新日期：2002-10-15 00:00:00
abstract：:Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9933
更新日期：1988-11-11 00:00:00
abstract：:Two residues are invariant in all bZip basic regions: asparagine -18 and arginine -10 (we define the first leucine of the leucine zipper of GCN4 as +1). X-ray structures of two specific GCN4-DNA complexes (Ellenberger et al., Cell, 71, 1223-1237, 1992; König & Richmond, J. Mol. Biol., 233, 139-154, 1993) demonstrate t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.21.4395
更新日期：1994-10-25 00:00:00
abstract：:Here we compare several methods for predicting oligonucleotide frequencies in 691 kb of Drosophila melanogaster DNA. As in previous work on Escherichia coli and Saccharomyces cerevisiae, a relatively simple equation based on tetranucleotide frequencies can be used in predicting frequencies of higher order oligonucleot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.14.3651
更新日期：1992-07-25 00:00:00
abstract：:Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.7.2407
更新日期：1977-07-01 00:00:00
abstract：:An examination, using reversed-phase chromatography and cyanogen bromide treatment, of tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp from SV40-transformed mouse fibroblasts grown to different cell densities, untransformed cells grown to confluence, and mouse liver indicates that: (1) The tissue cultured mouse fibroblasts exa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2513
更新日期：1978-07-01 00:00:00
